Bacterial community composition in breast cancer subtypes.

Abstract

e13063 Background: Breast cancer is a heterogeneous disease with multiple molecular subtypes and prognostic outcomes. Among these subtypes, Luminal-A is enriched with estrogen receptor and has the best clinical prognosis, whereas triple-negative breast cancer (TNBC) remains an aggressive subtype with poor prognosis. Changes in the diversity of breast microbiome have been associated with breast cancer initiation and progression. We hypothesized that Luminal-A and TNBC subtypes will have differences in both bacterial community composition as well as differences in microbial genomes and pathways. Methods: 6 Luminal-A and 6 TNBC FPPE tissue blocks were processed for both 16S V4 rRNA amplicon sequencing and shotgun metagenomics sequencing. 16S sequencing data was processed using mothur (v1.44.3) and reads were assigned taxonomy against the SILVA 16S rRNA database (v132). Shotgun sequencing was processed using the EBI-Metagenomic (v5) pipeline; bacterial identification was performed using the Kraken pipeline. Results: Shannon alpha-diversity or species enrichment, was significantly higher in Luminal-A compared to TNBC (nonparametric, P = 0.008) and their microbiome composition was significantly different by beta-diversity analysis (bray-curtis dissimilarity, PERMANOVA, P = 0.014). Bacteroides and Sphingomonadaceae species were significantly higher in abundance in Luminal-A, compared to Pseudomonas and Neisseriaceae species abundance in TNBC. Results were validated by shotgun sequencing. Luminal-A and TNBC bacterial metabolic pathways were not statistically different overall (PERMANOVA, P = 0.312). Pathways associated with Luminal-A included Response to Wounding (GO: 0009611), tRNA modification (GO: 0006400), and Cytoplasmic Microtubule Organization (GO: 0031122). Pathways associated with TNBC included troponin complex (GO: 0005861), rRNA processing (GO: 0006364), and CDC73 PAF1 (GO: 0016593). Conclusions: Using both shotgun and amplicon sequencing, this is the first analysis to show that Luminal-A and TNBC subtypes have statistically significant differences in bacterial species composition. Luminal-A had higher species diversity and abundance of Sphingomonadaceae, which are associated with healthy breast tissue and better clinical outcomes. TNBC had lower species diversity and abundance of Pseudomonas and Neisseriaceae, which have been associated with tumor survival and cell growth. Understanding the role of microbiota and its complex interaction with tumor microenvironment could help identify new treatment targets in breast cancer subtypes, and warrants further investigations.